PART / PART-up – Test for the Recurrence of Genomic Aberrations

PART / PART-up

:: DESCRIPTION

PART (parametric aberration recurrence test) is a new parametric method to test for the recurrence of genomic aberrations.

PART-up is an  extention of PART to cover unpaired data so that there is a statistical basis for analyzing unpaired genomic data.

::DEVELOPER

Atsushi Niida 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Perl
  • R package

:: DOWNLOAD

 PART / PART-up

:: MORE INFORMATION

Citation

Niida, A and Imoto, S and Shimamura, T and Miyano, S
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Bioinformatics, 2012, 28:i115-i120

DOMIRE – DOMain Identification from Recurrence

DOMIRE

:: DESCRIPTION

DOMIRE is a program using VAST to define the domain boundaries in proteins from their 3D structures with a list of structural neighbours.

::DEVELOPER

DOMIRE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DOMIRE: a web server for identifying structural domains and their neighbors in proteins.
Samson F, Shrager R, Tai CH, Sam V, Lee B, Munson PJ, Gibrat JF, Garnier J.
Bioinformatics. 2012 Apr 1;28(7):1040-1. doi: 10.1093/bioinformatics/bts076.

DNENRICH – A framework for Calculating Recurrence and Gene-set Enrichment for de novo Mutations

DNENRICH

:: DESCRIPTION

DNENRICH is a statistical software package for calculating gene set enrichment for de novo mutations (typically detected by exome sequencing) of a disease cohort.

::DEVELOPER

Menachem Fromer and Shaun Purcell

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Complier

:: DOWNLOAD

  DNENRICH

:: MORE INFORMATION

Citation

Fromer et al. (2014)
De novo mutations in schizophrenia implicate synaptic networks.
Nature 506(7487):179-84.

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